PRF/J: Chloroplast and Nuclear Sequence Phylogenetics of the Palmae

尽管对形态学、解剖学和分子数据集进行了深入的研究，但棕榈科内的系统发育关系和单子科内的家族位置仍未得到解决，这在具有深系统发育分支的分类群中很常见。解决这些问题的方法包括生成额外的数据集，增加分类单元的采样密度，对化石记录进行全面审查，以及对各种数据集进行单独和组合的批判性分析。为此目的，将寻求在家族、亚家族和分支水平上显示适合系统发育分辨率的差异水平的DNA区域。来自核和叶绿体基因组的序列将为该家族的代表成员和提出的外群分类群产生。数据分析既要独立进行，也要与不同的数据集相结合。系统发育重建将使用简约分析，并采用共识和组合方法。要解决的具体进化问题包括解决家族内部和单子房的系统发育位置，研究系统发育框架内的特征进化，基因组内部和跨基因组的比较分子进化，以及检查家族所表现出的广泛的生物地理模式。由于存在广泛的化石记录，并且该科通常具有很好的特征，仅限于热带/亚热带，并且传播能力较低，因此棕榈树为进行上述工作提供了极好的群体。本研究将探讨系统学中有关资料分析的争议性问题。问题是“什么是最合适的分析方法”。困难涉及：(a)一个数据集相对于另一个数据集的相对重要性和(b)基因、基因组和有机体系统发育的问题。关于分析策略的争论围绕着共识或组合的方法展开。这一领域的动态性表明，需要对潜在的解决方案进行更多的比较和应用。

Despite intensive study of morphological, anatomical and molecular data sets, phylogenetic relationships within the Palmae and the family position within the monocots remain unresolved, a situation common in taxa with deep phylogenetic branches. Solutions to such problems include generation of additional data sets, greater taxon sampling density, comprehensive review of the fossil record,and critical analysis of the various data sets individually and in combination. For this purpose, regions of DNA exhibiting levels of divergence appropriate for phylogenetic resolution at the familial, subfamilial and sectional levels will be sought. Sequences from both nuclear and chloroplast genomes will be produced for representative members of the family and proposed outgroup taxa. Analysis of data is to be conducted independently but also coupled with different data sets. Phylogenetic reconstruction will use parsimony analysis, and employ consensus and combinational approaches. Specific evolutionary issues to be addressed include resolution of phylogenetic position both within the family and with respect to the monocots, study of character evolution within a phylogenetic framework, comparative molecular evolution within and across genomes, and examination of broad biogeographic patterns exhibited by the family. %%% Because an extensive fossil record exists, and the family is generally well characterized, restricted to the tropics/subtropics, and has low dispersal abilities, the palms provide an excellent group for conducting the work described above. This study will address controversial problems involving data analysis in systematics. The issue is "What is the most appropriate method of analysis." Difficulties relate to: (a) relative importance of one data set compared to another and (b) questions of gene versus genome versus organismal phylogenies. Debate over analytical strategies revolves around methods of consensus or combination. The dynamic nature of this field indicating that additional comparisons and applications of potential solutions are needed.